Mine has been doing the same. Thought it was just me. My email and SMS contact notifications would change to a different sound. They were my own custom ring tones I placed on my sdcard. Don't have that problem if I use system ringtones. Ended up using Root Explorer to place my favorite ring tones in the system audio folder. So far I haven't had the issue again.
Not sure if Power Amp is causing the problem. It was the last app I installed before the issue happened. Or it could very well be another app that's causing it.
I am too and have latest OS from vzw. Just got my 2nd refurb phone per vzw who is blaming hardware for the issue. More people need to call and report problem before they will even look at OS again.
Try unmounting your SD card, and then remount it. I was having the same problem with my unrooted HTC EVO 3D, and the majority of my ringtones are custom as well. I unmounted the SD card then remounted it and so far so good I have not yet had an issue.